def electron_affinity(symb, add, electrons=1.0):
""" Return electron affinity of given atom.
parameters:
-----------
symb: element symbol
add: orbital where electron is added (e.g. '2p')
electrons: how many electrons are added. Can be fractional number
if DFT should not be stable. EA is scaled by
electrons^-1 in the end to extrapolate to electrons=1.
"""
from box.data import atom_occupations
occu = atom_occupations[symb].copy()
# neutral atom
atom = KSAllElectron(symb)
atom.run()
e0 = atom.get_energy()
# positive ion
occu[add] += electrons
ion = KSAllElectron(symb, occu=occu)
ion.run()
e1 = ion.get_energy()
return (e0 - e1) / electrons
def ionization_potential(symb, remove, electrons=1.0):
""" Return ionization potential of given atom.
parameters:
-----------
symb: element symbol
remove: orbital from where electron is removed (e.g. '2p')
electrons: how many electrons to remove. Can be fractional number
if DFT should not be stable. IP is scaled by
electrons^-1 in the end to extrapolate to electrons=1.
"""
from box.data import atom_occupations
occu = atom_occupations[symb].copy()
# neutral atom
atom = KSAllElectron(symb)
atom.run()
e0 = atom.get_energy()
# negative ion
occu[remove] -= electrons
ion = KSAllElectron(symb, occu=occu)
ion.run()
e1 = ion.get_energy()
return (e1 - e0) / electrons
def electron_affinity(symb,add,electrons=1.0):
""" Return electron affinity of given atom.
parameters:
-----------
symb: element symbol
add: orbital where electron is added (e.g. '2p')
electrons: how many electrons are added. Can be fractional number
if DFT should not be stable. EA is scaled by
electrons^-1 in the end to extrapolate to electrons=1.
"""
from box.data import atom_occupations
occu=atom_occupations[symb].copy()
# neutral atom
atom=KSAllElectron(symb)
atom.run()
e0=atom.get_energy()
# positive ion
occu[add]+=electrons
ion=KSAllElectron(symb,occu=occu)
ion.run()
e1=ion.get_energy()
return (e0-e1)/electrons
def ionization_potential(symb,remove,electrons=1.0):
""" Return ionization potential of given atom.
parameters:
-----------
symb: element symbol
remove: orbital from where electron is removed (e.g. '2p')
electrons: how many electrons to remove. Can be fractional number
if DFT should not be stable. IP is scaled by
electrons^-1 in the end to extrapolate to electrons=1.
"""
from box.data import atom_occupations
occu=atom_occupations[symb].copy()
# neutral atom
atom=KSAllElectron(symb)
atom.run()
e0=atom.get_energy()
# negative ion
occu[remove]-=electrons
ion=KSAllElectron(symb,occu=occu)
ion.run()
e1=ion.get_energy()
return (e1-e0)/electrons
from hotbit.parametrization.util import IP_EA
from box.mix import Timer
#import cgitb; cgitb.enable()
import pylab as pl
#IP=ionization_potential('C',remove='2p')
IP, EA = IP_EA('O', remove_orb='2p', add_orb='2p', remove=1.0, add=0.5)
print(IP, IP * 27.2114, IP * 27.2114 / 0.01036)
print(EA, EA * 27.2114, EA * 27.2114 / 0.01036)
raise SystemExit
for i, element in enumerate(['H', 'C', 'Ti', 'Au']):
e = {}
per = [100, 150, 200, 250, 300, 400, 500, 1000]
for pernode in per:
atom = KSAllElectron(element, pernode=pernode)
v = atom.get_valence()
if e == {}:
for val in v:
e[val] = []
atom.run()
for val in v:
e[val].append(atom.get_eigenvalue(val))
pl.subplot(2, 2, i + 1)
for val in v:
#pl.plot(per,e[val]-e[val][-1],label=val)
pl.semilogy(per, e[val] - e[val][-1] + 1E-6, label=val)
pl.legend()
pl.xlabel('points/node')
from hotbit.parametrization import KSAllElectron, SlaterKosterTable
atom = KSAllElectron(
'C',
xc='PBE',
confinement={
'mode': 'Woods-Saxon',
'r0': 8.,
'a': 4.,
'W': 0.75
},
)
atom.run()
atom.plot_Rnl()
table = SlaterKosterTable(atom, atom)
table.run(R1=1, R2=10, N=3, ntheta=50, nr=10)
table.plot()
from hotbit.parametrization import SlaterKosterTable
from hotbit.parametrization import KSAllElectron
from util import plot_table
from hotbit import Element
from pickle import load
import pylab as pl
from box.data import data
e1=KSAllElectron('C',confinement={'mode':'quadratic','r0':5.04})
e1.run()
e2=KSAllElectron('H',confinement={'mode':'quadratic','r0':5.04})
e2.run()
sk=SlaterKosterTable(e1,e2)
sk.run(1,15,20,ntheta=50,nr=25)
sk.write()
plot_table('C_H.par',screen=True)
#sk.run(1,15,50)
#sk.write()
#compare_tables('Au_Au.par','Au_Au_NR.par',s1='Au',s2='Au',screen=False)
lst=[('C','C',1.85*1.46,1.85*1.46),\
('C','H',1.85*1.46,1.85*0.705),\
('Na','C',1.85*2.9,1.85*1.46),\
('O','H',1.85*1.38,1.85*0.705),\
('Mg','O',1.85*1.41/0.529177,1.85*1.38),\
('Na','O',1.85*2.9,1.85*1.38),\
('H','H',1.85*0.705,1.85*0.705)]
for s1,s2,r01,r02 in lst:
e1=KSAllElectron(s1,nodegpts=500,confinement={'mode':'quadratic','r0':r01})
e1.run()
if s1==s2:
e2=e1
else:
e2=KSAllElectron(s2,confinement={'mode':'quadratic','r0':r02})
e2.run()
sk=SlaterKosterTable(e1,e2)
sk.run(1E-3,12,10) #,ntheta=20,nr=20)
sk.write()
file='%s_%s.par' %(s1,s2)
#compare_tables( param+'/'+file,file,s1,s2,screen=False)
plot_table(file,s1=s1,s2=s2,screen=True,der=0)
plot_table(file,s1=s1,s2=s2,screen=True,der=1)
from hotbit.parametrization import KSAllElectron, SlaterKosterTable
atom=KSAllElectron('C',convergence={'density':1E-1,'energies':1E-1},txt='/dev/null')
atom.run()
table=SlaterKosterTable(atom,atom,txt='/dev/null')
table.run(R1=1,R2=10,N=3,ntheta=50,nr=10,wflimit=1E-7)
def IP_EA(symb, remove_orb, add_orb, remove, add, add_args={}):
""" Return ionization potential and electron affinity for given atom,
and the valence energies of neutral atom.
parameters:
-----------
symb: element symbol
remove_orb: orbital from where to remove atoms (e.g. '2p')
add_orb: orbital from where to add atoms (e.g. '2p')
remove: how many electrons to remove
add: how many electrons to add
(remove and add can be different from 1.0 if DFT should not
be stable to e.g. adding one full electron)
Fit second order curve for 3 points and return IP and EA for full
electron adding and removal.
"""
#from box.data import atom_occupations
atom = KSAllElectron(symb, txt='-', **add_args)
# add electrons -> negative ion
#occu=atom_occupations[symb].copy()
w = 'negative.atom'
occu_add = atom.occu.copy()
occu_add[add_orb] += add
ea = KSAllElectron(symb,
configuration=occu_add,
restart=w,
write=w,
**add_args)
ea.run()
# neutral atom
w = 'neutral.atom'
neutral = KSAllElectron(symb, restart=w, write=w, **add_args)
neutral.run()
valence_energies = neutral.get_valence_energies()
# remove electrons -> positive ion
#occu=atom_occupations[symb].copy()
w = 'positive.atom'
occu_remove = atom.occu.copy()
occu_remove[remove_orb] -= remove
ip = KSAllElectron(symb,
configuration=occu_remove,
restart=w,
write=w,
**add_args)
ip.run()
e0 = neutral.get_energy()
en = ea.get_energy() - e0
ep = ip.get_energy() - e0
# e(x)=e0+c1*x+c2*x**2 =energy as a function of additional electrons
c2 = (en + ep * add / remove) / (add * (remove + add))
c1 = (c2 * remove**2 - ep) / remove
IP = -c1 + c2
EA = -(c1 + c2)
return IP, EA, neutral
def IP_EA(symb,remove_orb,add_orb,remove,add,add_args={}):
""" Return ionization potential and electron affinity for given atom,
and the valence energies of neutral atom.
parameters:
-----------
symb: element symbol
remove_orb: orbital from where to remove atoms (e.g. '2p')
add_orb: orbital from where to add atoms (e.g. '2p')
remove: how many electrons to remove
add: how many electrons to add
(remove and add can be different from 1.0 if DFT should not
be stable to e.g. adding one full electron)
Fit second order curve for 3 points and return IP and EA for full
electron adding and removal.
"""
#from box.data import atom_occupations
atom = KSAllElectron(symb, txt='-', **add_args)
# add electrons -> negative ion
#occu=atom_occupations[symb].copy()
w = 'negative.atom'
occu_add = atom.occu.copy()
occu_add[add_orb] += add
ea = KSAllElectron(symb, configuration=occu_add, restart=w, write=w,
**add_args)
ea.run()
# neutral atom
w = 'neutral.atom'
neutral = KSAllElectron(symb, restart=w, write=w, **add_args)
neutral.run()
valence_energies = neutral.get_valence_energies()
# remove electrons -> positive ion
#occu=atom_occupations[symb].copy()
w = 'positive.atom'
occu_remove = atom.occu.copy()
occu_remove[remove_orb] -= remove
ip = KSAllElectron(symb, configuration=occu_remove, restart=w, write=w,
**add_args)
ip.run()
e0 = neutral.get_energy()
en = ea.get_energy()-e0
ep = ip.get_energy()-e0
# e(x)=e0+c1*x+c2*x**2 =energy as a function of additional electrons
c2 = (en+ep*add/remove)/(add*(remove+add))
c1 = (c2*remove**2-ep)/remove
IP = -c1+c2
EA = -(c1+c2)
return IP, EA, neutral
from hotbit.parametrization import KSAllElectron, SlaterKosterTable
atom = KSAllElectron('C',
convergence={
'density': 1E-1,
'energies': 1E-1
},
txt='/dev/null')
atom.run()
table = SlaterKosterTable(atom, atom, txt='/dev/null')
table.run(R1=1, R2=10, N=3, ntheta=50, nr=10, wflimit=1E-7)
from hotbit.parametrization.util import IP_EA
from box.mix import Timer
#import cgitb; cgitb.enable()
import pylab as pl
#IP=ionization_potential('C',remove='2p')
IP, EA=IP_EA('O',remove_orb='2p',add_orb='2p',remove=1.0,add=0.5)
print IP,IP*27.2114,IP*27.2114/0.01036
print EA,EA*27.2114,EA*27.2114/0.01036
raise SystemExit
for i,element in enumerate(['H','C','Ti','Au']):
e={}
per=[100,150,200,250,300,400,500,1000]
for pernode in per:
atom=KSAllElectron(element,pernode=pernode)
v=atom.get_valence()
if e=={}:
for val in v:
e[val]=[]
atom.run()
for val in v:
e[val].append(atom.get_eigenvalue(val))
pl.subplot(2,2,i+1)
for val in v:
#pl.plot(per,e[val]-e[val][-1],label=val)
pl.semilogy(per,e[val]-e[val][-1]+1E-6,label=val)
pl.legend()
pl.xlabel('points/node')
